In RGLab/HIPCCyto: HIPC Cytometry

library(flexdashboard)
library(gtools)
library(ImmPortR)
library(semver)
library(aws.s3)
library(jsonlite)
library(reactable)

url <- "https://fh-pi-gottardo-r-eco-public.s3-us-west-2.amazonaws.com/hipccyto"
dev <- params$dev
immport <- params$immport
data_dir <- "/fh/fast/gottardo_r/HIPCCyto/data"
studies <- mixedsort(dir(data_dir, pattern = "SDY\\d+"))
checks <- lapply(studies, function(sdy) {
  res <- data.frame(
    study = sdy,
    pi = NA,
    condition_studied = NA,
    hipc = NA,
    gating_sets = NA,
    version = NA,
    downloaded = FALSE,
    pre_processed = FALSE,
    reviewed = NA,
    faust = NA,
    uploaded = NA,
    number_of_files = NA,
    size = NA
  )

  # get study summary
  if (isTRUE(immport)) {
    summary <- try(query_study_summary(sdy))
    if (!is(summary, "try-error")) {
      res$pi <- summary$pi
      res$condition_studied <- summary$conditionStudied
      res$hipc <- grepl("HIPC", summary$program)
    }
  }

  # fcs files downloaded?
  fcs <- dir(
    path = file.path(data_dir, sdy, "ResultFiles/Flow_cytometry_result"),
    pattern = ".fcs",
    full.names = TRUE
  )
  if (length(fcs) == 0) {
    return(res)
  }
  res$downloaded <- TRUE
  res$number_of_files <- length(fcs)
  res$size <- sum(file.info(fcs)$size)

  # pre-processed?
  sdy_dir <- file.path(data_dir, sdy, "GatingSets")
  versions <- dir(sdy_dir, pattern = "^v\\d+.\\d+.\\d+$")
  if (length(versions) == 0) {
    return(res)
  }
  latest <- versions[order(parse_version(gsub("^v", "", versions)), decreasing = TRUE)][1]
  ver_dir <- file.path(sdy_dir, latest)
  completed <- file.exists(file.path(ver_dir, "study.html"))
  if (isFALSE(completed)) {
    return(res)
  }
  res$pre_processed <- TRUE
  res$version <- latest

  # uploaded?
  uploaded <- object_exists(
    object = file.path(sdy, "GatingSets", latest, "study.html"),
    bucket = "fh-pi-gottardo-r-eco-public/hipccyto",
    region = "us-west-2"
  )
  if (isTRUE(uploaded)) {
    res$uploaded <- TRUE
    study_html <- file.path(url, sdy, "GatingSets", latest, "study.html")
    res$study <- paste0("<a href='", study_html, "'>", sdy, "</a>")
  } else {
    res$uploaded <- FALSE
  }

  # reviewed?
  gs_dirs <- dir(file.path(ver_dir), pattern = "^gs\\d+$", full.names = TRUE)
  reviewed <- sapply(gs_dirs, function(path) {
    file.exists(file.path(path, "QC_original.html"))
  })
  res$reviewed <- all(reviewed == TRUE)

  # get gating sets
  gating_sets <- sapply(mixedsort(gs_dirs), function(gs_dir) {
    summary <- read_json(file.path(gs_dir, "summary"))
    markers <- paste(summary$markers, collapse = " | ")
    gs_accession <- summary$gs_accession
    if (isTRUE(uploaded)) {
      qc_html <- file.path(url, sdy, "GatingSets", latest, gs_accession, "QC.html")
      gs_accession <- paste0("<a href='", qc_html, "'>", gs_accession, "</a>")
    }
    paste0(gs_accession, ": ", markers)
  })
  res$gating_sets <- paste(unname(gating_sets), collapse = "<br>")

  # faust results?
  faust <- dir.exists(file.path(data_dir, sdy, "FAUST", latest))
  res$faust <- faust

  res
})

df <- do.call(rbind, checks)

total_size <- utils:::format.object_size(sum(df$size, na.rm = TRUE), "auto")
total_files <- sum(df$number_of_files, na.rm = TRUE)
df$size <- sapply(df$size, function(x) {
  if (is.na(x)) return(NA); utils:::format.object_size(x, "auto")
})

Row

fcs files (`r total_size`)

valueBox(total_files, icon = "fa-file")

Pre-processed

get_sectors <- function(n) {
  gaugeSectors(
    success = c(ceiling(n * 0.8), n),
    warning = c(ceiling(n * 0.4), floor(n * 0.8)),
    danger = c(0, floor(n * 0.4))
  )
}
n <- nrow(df)
n_processed <- sum(df$pre_processed, na.rm = TRUE)
gauge(
  value = n_processed,
  min = 0, max = n,
  sectors = get_sectors(n),
  label = "studies"
)

Reviewed

n_reviewed <- sum(df$reviewed, na.rm = TRUE)
gauge(
  value = n_reviewed,
  min = 0, max = n_processed,
  sectors = get_sectors(n_processed),
  label = "studies"
)

FAUST

n_faust <- sum(df$faust, na.rm = TRUE)
gauge(
  value = n_faust,
  min = 0, max = n_reviewed,
  sectors = get_sectors(n_reviewed), label = "studies"
)

Row

style <- function(value) {
  list(
    color = ifelse(isTRUE(value), "green", "red"),
    fontWeight = ifelse(isTRUE(value), "bold", "normal"))
}
reactable(
  data = df,
  filterable = TRUE,
  sortable = FALSE,
  columns = list(
    study = colDef(html = TRUE),
    pi = colDef(show = dev, minWidth = 150),
    condition_studied = colDef(html = TRUE, minWidth = 150),
    hipc = colDef(style = style),
    gating_sets = colDef(html = TRUE, minWidth = 750),
    downloaded = colDef(show = dev, style = style),
    pre_processed = colDef(minWidth = 140, style = style),
    reviewed = colDef(style = style),
    faust = colDef(style = style),
    uploaded = colDef(show = dev, style = style),
    number_of_files = colDef(
      sortable = TRUE, filterable = FALSE, show = dev, minWidth = 150
    ),
    size = colDef(show = dev, filterable = FALSE)
  ),
  pagination = FALSE,
  resizable = TRUE
)